Re: [XMLPipeDB-developer] Info table
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Re: [XMLPipeDB-developer] Info table
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From: Richard B. <rbr...@gm...> - 2011-08-16 22:32:52
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OK, so its pretty much the last line of getSystemsTableManager() which needs
to be modified to be aware of the collection of SpeciesProfile:
tableManager = speciesProfile.getSystemsTableManagerCustomizations(tableManager,
*this*);
*return* tableManager;
So I believe I need to iterate through each species of the collection before
returning the final tableManager.
I would enclose it in a for loop ( SpeciesProfile speciesProfile :
speciesProfiles ) {
}
This would seem to be the correct implementation to ensure that each species
customization would be applied.
Sound good??
Richard
On Tue, Aug 16, 2011 at 12:38 PM, Richard Brous <rbr...@gm...> wrote:
> gotcha, heading to system tables.
>
> gotcha.
>
> gotcha.
>
> Thanks for the speedy reply =D
>
> Richard
>
> On Tue, Aug 16, 2011 at 12:21 PM, John David N. Dionisio <do...@lm...>wrote:
>
>> Hi Rich,
>>
>> Yeah, relations is pretty complicated. I suggest you skip that and go to
>> just the system tables for now (i.e., the tables that hold the IDs
>> themselves). The relationship tables hold pairs of IDs (i.e., which one
>> from one system corresponds to the ID from another) and so is an additional
>> level of complexity, I think.
>>
>> Regarding your prior question about the Info table --- I'm not or'ing the
>> species names. I'm merely concatenating the names with pipes ("|") in
>> between, as Kam specified. While the final value may look like an "or," it
>> is ultimately just a string. The "|" could just have easily been a comma,
>> semicolon, or other separator.
>>
>> Your prior guess as to how that would look, with the multiple { "Species",
>> speciesName } pairs, would actually be equivalent to multiple values for the
>> single Species column, which does not fit the relational model. The Species
>> column can have only one value, and in this case it is a single string that
>> is the concatenation of all selected species names, separated by "|"
>> characters.
>>
>> Hope that clears things up...
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>
>>
>> On Aug 16, 2011, at 12:11 PM, Richard Brous wrote:
>>
>> > OK, have moved onto getRelationsTableManager() ... this one seems pretty
>> complicated...
>> >
>> > Have reviewed the method and submethods called and have the following
>> questions:
>> >
>> > 1. What are the RelationshipTables that are stored in
>> relationshipTables?
>> > aren't they species dependent? Can't seem to find where they were
>> created?
>> > If not, then:
>> >
>> > 2. How should the if/else conditional be handled?
>> >
>> > if
>> >
>> >
>> (speciesProfile.getSpeciesSpecificSystemTables().containsKey(stp.systemTable1)
>> |
>> >
>> >
>> speciesProfile.getSpeciesSpecificSystemTables().containsKey(stp.systemTable2))
>> {
>> > tableManager =
>> >
>> > speciesProfile.getRelationsTableManagerCustomizations(stp.systemTable1,
>> > stp.
>> >
>> > systemTable2, templateDefinedSystemToSystemCode, tableManager);
>> > This obviously needs to be made aware of Lists of SpeciesProfiles... to
>> build the correct tableManager, do I need this conditional to run through
>> every species or should we enclose all the code (if and else) within a loop
>> through each species?
>> >
>> > Thanks.
>> >
>> > Richard
>> >
>> >
>> > On Tue, Aug 16, 2011 at 11:02 AM, Richard Brous <rbr...@gm...>
>> wrote:
>> > Sorry I typed and sent that out too quickly before getting my thoughts
>> completely together...
>> >
>> > First off i thought that the array[][] portion of the submit needed to
>> be in the following format: { "Species", speciesName1 }, { "Species",
>> speciesName2 }, { "Species", speciesName3 },...
>> > but I see you specified it as: { "Species", speciesName1 | speciesName2
>> | speciesName3 }, ... OR'ing each of the species names?
>> >
>> > I see what you did regarding the date object... yes no reason to
>> recreate a second object...
>> >
>> > As mentioned previously I will continue through the next methods,
>> submitting (well thought out) changes and emailing out updates...
>> >
>> > Richard
>> > On Tue, Aug 16, 2011 at 10:36 AM, Richard Brous <rbr...@gm...>
>> wrote:
>> > Took a look at your code and realized what I had done wrong. I should
>> have just broken out the loop as the second argument of the 3 in the submit
>> method. That was a rookie move on my part.
>> >
>> > I am moving on to the next method and will keep my mind on the syntactic
>> solution that I'm not thinking through prior to moving forward with an
>> implementation.
>> >
>> > Richard
>> >
>> > On Mon, Aug 15, 2011 at 1:30 AM, John David N. Dionisio <do...@lm...>
>> wrote:
>> > OK, everything is committed. I got up to the tweaks on the second panel
>> in the wizard (Save As/GO Aspects), as well as the query change for
>> exporting any combination of C, F, or P.
>> >
>> > I still have to do the GO OBO format check, plus the UI work on the
>> remaining two wizard panels. But meanwhile, hope these latest changes work
>> out well.
>> >
>> > John David N. Dionisio, PhD
>> > Associate Professor, Computer Science
>> > Loyola Marymount University
>> >
>> >
>> >
>> > On Aug 14, 2011, at 7:31 PM, Richard Brous wrote:
>> >
>> > > OK, using option 2 I have made changes to DatabaseProfile.java to
>> allow for all species names to be included in the submit argument.
>> > > But I'm stuck on how to change my StringBuilder object to a type that
>> submit wants. Help please!!
>> > >
>> > > Submitted the above and some comment changes to SourceForge this
>> evening.
>> > >
>> > > Richard
>> > >
>> > > On Fri, Aug 12, 2011 at 12:08 PM, Kam Dahlquist <kda...@lm...>
>> wrote:
>> > > Hi,
>> > >
>> > > I think we had better leave the info table with only one record
>> > > (option 2). The species names can be separated by pipes " | " as
>> > > they are in the Systems table where there are multiple species. To
>> > > my knowledge, the only time GenMAPP needs to access the info table is
>> > > for the "DisplayOrder" field, I don't know what would happen if there
>> > > were multiple records there. I know that the spec for the table says
>> > > that it should only be one record, but I don't know if it would crash
>> > > if there were multiple records. To be on the safe side, I think we
>> > > should just keep it to the one record.
>> > >
>> > > Best,
>> > > Kam
>> > >
>> > > At 09:45 PM 8/10/2011, John David N. Dionisio wrote:
>> > > >Greetings,
>> > > >
>> > > >I think we have to turn to Dr. Dahlquist's GenMAPP knowledge here to
>> > > >get the definitive answer. I see two choices:
>> > > >
>> > > >- The Info table should have one record for each species that the
>> > > >.gdb holds, in which case the change you need is to wrap that single
>> > > >submit call inside a loop, so that submit is called once for each
>> > > >chosen species.
>> > > >
>> > > >- The Info table should always have one record, and if the .gdb
>> > > >holds multiple species, the "Species" column should be some
>> > > >concatenation of multiple species names. In this case, you would
>> > > >still call submit only once, but the value you send into the
>> > > >"Species" column is some accumulation of all chosen species names.
>> > > >
>> > > >Admittedly I don't know which way is right (I assumed the former as
>> > > >of our Tuesday meeting, but on further examination I'm no longer
>> > > >quite so sure).
>> > > >
>> > > >For Kam --- what does GenMAPP expect to see in the Info table if the
>> > > >opened .gdb contains multiple species?
>> > > >
>> > > >John David N. Dionisio, PhD
>> > > >Associate Professor, Computer Science
>> > > >Loyola Marymount University
>> > > >
>> > > >
>> > > >On Aug 10, 2011, at 9:36 PM, Richard Brous wrote:
>> > > >
>> > > > > OK, continued to review ExportToGenMAPP and dug into the creation
>> > > > of the first TableManager tmA on line 118.
>> > > > >
>> > > > > In reading through the method, my understanding is that it
>> > > > creates a new TableManager based on the selectedDatabaseProfile
>> > > > (which is UniProt).
>> > > > >
>> > > > > This is performed by the method getInfoTableManager() which then
>> > > > calls method submit(String tableName, QueryType queryType,
>> > > > String[][] columnNamesToValues);
>> > > > >
>> > > > > the code is as follows:
>> > > > >
>> > > > > tableManager.submit("Info", QueryType.insert, new String[][] { {
>> > > > "Owner", owner }, { "Version", new
>> > > > SimpleDateFormat("yyyyMMdd").format(version) }, { "MODSystem",
>> > > > modSystem }, { "Species", speciesProfile.getSpeciesName() }, {
>> > > > "Modify", new SimpleDateFormat("yyyyMMdd").format(modify) }, {
>> > > > "DisplayOrder", displayOrder }, { "Notes", notes } });
>> > > > >
>> > > > >
>> > > > > The modification of this line centers on { "Species",
>> > > > speciesProfile.getSpeciesName() }, since it originally processed a
>> > > > single species.
>> > > > >
>> > > > > So now I need to populate the arguments with the species
>> > > > contained within selectedDatabaseprofile.selectedSpeciesProfiles.
>> > > > >
>> > > > > I think I'll start with the baseArgument up to MODSystem, then
>> > > > append as many species as necessary, and then cap off the end with
>> > > > the rest starting at Modify. (similar to your approach in
>> > > > ExportGoData, populateUniprotGoTableFromSQL(char chosenAspect,
>> > > > List<Integer> taxonIds) line 513
>> > > > >
>> > > > > Please let me know if this approach or analysis is off track.
>> > > > >
>> > > > > Thanks!
>> > > > >
>> > > > > Richard
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > On Wed, Aug 10, 2011 at 5:50 PM, Richard Brous <
>> rbr...@gm...> wrote:
>> > > > > Updated repository to include all Gene Ontology changes discussed
>> > > > during our meeting yesterday.
>> > > > >
>> > > > > Digging into TableManager next.
>> > > > >
>> > > > > Richard
>> > > > >
>> > > > > On Fri, Aug 5, 2011 at 10:06 AM, Richard Brous <
>> rbr...@gm...> wrote:
>> > > > > whew... thanks for the detailed reply. I will digest this a bit
>> > > > and get back to you with further questions.
>> > > > >
>> > > > > rb
>> > > > >
>> > > > > On Thu, Aug 4, 2011 at 11:18 PM, John David N. Dionisio
>> > > > <do...@lm...> wrote:
>> > > > > Greetings,
>> > > > >
>> > > > > Sorry for the delay. I wasn't able to walk through the relevant
>> > > > code until this evening.
>> > > > >
>> > > > > As Kam said, GOA serves as the link between the UniProt and GO
>> > > > IDs. It essentially determines which GO IDs get exported by using
>> > > > GOA to see which GO IDs are associated with an exported UniProt
>> > > > ID. The populateUniprotGoTableFromSQL, in its current form,
>> > > > extracts the GO association records that match the given taxon ID
>> > > > then exports, as UniProt-GO pairs, the GO and UniProt IDs
>> > > > referenced within that GO association record. Processing that
>> > > > follows this is then based on the GO IDs that got exported --- and
>> > > > that's how the current code avoids exporting the entire list of GO
>> terms.
>> > > > >
>> > > > > The operative query is on the second line of
>> populateUniprotGoTableFromSQL:
>> > > > >
>> > > > > String uniProtAndGOIDSQL = "select db_object_id, go_id,
>> > > > evidence_code, with_or_from from goa where db like '%UniProt%' and
>> > > > taxon = 'taxon:" + taxon + "'";
>> > > > >
>> > > > > In plain English, this selects the GOA records whose database is
>> > > > UniProt and whose taxon ID is the given taxon. An additional
>> > > > condition is added for the "aspect" (All, Component, Function, or
>> > > > Process) that is to be exported. This is another reduction filter,
>> > > > to further shrink the number of exported GO terms and thus avoid
>> > > > MAPPFinder issues later on.
>> > > > >
>> > > > > Given this, the proper expansion here is to change the taxon
>> > > > predicate to a multiple predicate. That is, this method can be
>> > > > changed to now accept a collection or array of taxon IDs, and the
>> > > > base query should then be changed so that it accepts any taxon from
>> > > > that collection. More or less, you want:
>> > > > >
>> > > > > private void populateUniprotGoTableFromSQL(char chosenAspect,
>> > > > int[] taxons) throws SQLException {
>> > > > >
>> > > > > ...then, instead of the single string, you want to iterate
>> > > > through the taxon IDs:
>> > > > >
>> > > > > StringBuilder baseQueryBuilder = new StringBuilder("select
>> > > > db_object_id, go_id, evidence_code, with_or_from from goa where db
>> > > > like '%UniProt%'");
>> > > > > boolean first = true;
>> > > > > for (int taxon: taxons) {
>> > > > > baseQueryBuilder.append(first ? " and (" : " or ");
>> > > > > baseQueryBuilder
>> > > > > .append("taxon = 'taxon:")
>> > > > > .append(taxon).append("'");
>> > > > > first = false;
>> > > > > }
>> > > > > baseQueryBuilder.append(")");
>> > > > >
>> > > > > ...and so on. I just sort of rattled this off so there may be
>> > > > little glitches, but anyway this is just to give you an overall
>> idea.
>> > > > >
>> > > > > Put another way, no, you do not need to iterate this method for
>> > > > each taxon ID. Instead, you can still call this method once, with
>> > > > the multiplicity of taxon IDs emerging in terms of the actual
>> > > > condition used for selecting the GO terms to be exported (based on
>> > > > the available GOA records, which as you may recall are loaded from
>> .goa files).
>> > > > >
>> > > > > As a side note, right here you have an opportunity for a little
>> > > > sanity check regarding the content of the relational database: GO
>> > > > terms will only be exported if GOA records for the desired taxon
>> > > > IDs have been imported into the database. So, as a pre-flight
>> > > > check, one can see if there are any GOA records at all for each
>> > > > chosen taxon ID. If there are none, then the .goa file for that
>> > > > species needs to be imported into the relational database.
>> > > > >
>> > > > > Hope this helps...
>> > > > >
>> > > > > John David N. Dionisio, PhD
>> > > > > Associate Professor, Computer Science
>> > > > > Loyola Marymount University
>> > > > >
>> > > > >
>> > > > > On Aug 4, 2011, at 1:00 PM, Kam Dahlquist wrote:
>> > > > >
>> > > > > > Hi,
>> > > > > >
>> > > > > > Dondi will have to chime in on this, but I think this is where
>> > > > things are going to get tricky.
>> > > > > >
>> > > > > > The final gdb does not actually contain the entire GO, it gets
>> > > > trimmed somehow based on the GO associations for a particular
>> > > > species. This is because MAPPFinder cannot handle loading the
>> > > > entire GO. Since there is some type of species-specific trimming
>> > > > going on, it's quite possible that this will need to iterate.
>> > > > > >
>> > > > > > However, I don't have the foggiest idea of how this works, so
>> > > > Dondi will have to chime in.
>> > > > > >
>> > > > > > Best,
>> > > > > > Kam
>> > > > > >
>> > > > > > At 12:09 AM 8/4/2011, you wrote:
>> > > > > >> Wednesday 8/3/11 progress:
>> > > > > >>
>> > > > > >> 1. After following the ExportPanel1.java ground zero code of:
>> > > > databaseProfile.setSelectedSpeciesProfile( selectedProfile );
>> > > > > >>
>> > > > > >> I found the method in DatabaseProfile.java plus a getter
>> method;
>> > > > > >> SpeciesProfile setSelectedSpeciesProfile( speciesProfile ) and
>> > > > SpeciesProfile getSelectedSpeciesProfile( speciesProfile )
>> > > > > >>
>> > > > > >> I created two new methods that each handle List<Object> of
>> > > > SpeciesProfiles argument instead of a single SpeciesProfile;
>> > > > setSelectedSpeciesProfiles and getSelectedSpeciesProfiles.
>> > > > > >>
>> > > > > >> This enabled the ExportPanel1 ground zero code to become:
>> > > > databaseProfile.setSelectedSpeciesProfiles(selectedSpecies);
>> > > > > >>
>> > > > > >> 2. public static void export() on line 104 in
>> ExportToGenMAPP.java
>> > > > > >>
>> > > > > >> On line 107 ExportGoData is instantiated which I found in
>> > > > ExportGoData.java and calls a method: public void export(char
>> > > > chosenAspect, int taxon).
>> > > > > >>
>> > > > > >> Within export, taxon id is required for another method:
>> > > > private void populateGoTables(char chosenAspect, int taxon).
>> > > > > >>
>> > > > > >> Within populateGoTables, taxon id is required for another
>> > > > method: private void populateUniprotGoTableFromSQL( char
>> > > > chosenAspect, int taxon).
>> > > > > >>
>> > > > > >> But, if the export to GDB process starts off with exporting GO
>> > > > data, doesn't it only need to do that once no matter how many
>> > > > species are selected? As you probably realize, I'm leading towards
>> > > > not having to iterate through this for each taxon id if possible.
>> > > > > >>
>> > > > > >> Also, how does the export actually work? How are GO ids and
>> > > > UniProt ids related within the table?
>> > > > > >>
>> > > > > >> Thanks!
>> > > > > >>
>> > > > > >> Richard
>> > > > > >>
>> > > > > >>
>> > > > > > <ATT00001..txt><ATT00002..txt>
>> > > > >
>> > > > >
>> > > > >
>> > > >
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